When Ben submits his request to identify the shark tooth to the bulletin board, he titles the message "Mystery Shark". When Cat finds it, it's titled "Mistery Shark". In the following close-up when she's reading it, it's titled "Mystery Shark" again.
When Ben is taking a picture of the shark tooth to send off for analysis, he snaps a photo with his digital camera, and without connecting the camera to his computer the picture magically appears. The photo has no background and, mysteriously, Ben's fingers are not on the tooth.
When the parasailing woman is being attacked by the shark, she goes from holding on to Cat's hand to under her parachute to holding Cat's hand again between shots.
During one sequence, Ben moves the throttle lever all the way up several times without moving it down in between.
When mama megalodon attacks boats, its teeth are twice bigger, than human's head. When Ben collects one tooth, it is a size of a hand.
Sharks do not roar.
The megalodon tooth featured is actually not megalodon: it is laterally compressed, lacking a scar and fine serrations, and does not have a v-shaped root. The tooth shown appears to be a member of the genus Isurus, the mako, or possibly what most scientists identify as the great white's true ancestor, Cosmopolitodus.
At the start of the movie, a lobster is caught off the coast of Mexico with large claws. Mexican lobsters are "spiny" lobsters which do not have claws. Maine lobsters have claws and are not found in Mexico.
After Ben locks somehow remotely redirects the fired torpedo to the submersible's position, he exits the sub via the main hatch. This would've been physically impossible unless the sub was completely flooded, which it wasn't.
At the beginning the shark attacks and kills a diver supposedly operating at a depth of 1,500 feet. The footage of the shark eating the diver is that of a great white thrashing on the surface.
The size of the megalodon keeps changing throughout the film.
A submarine in which characters travel is much bigger on the inside, than on the outside.
The megalodon appears, and in signaling for help Ben shoots a flare into the sky, which catches the attention of Hector flying in the helicopter. In the reaction shot of Hector (shown from outside of the helicopter) there is a reflection of a fence on the side of the helicopter. Ben is signaling for help out in the ocean.
When the megalodon is attacking the yacht and the party goers are jumping off, some make it to a huge inflatable safety raft. Off to the right of the safety raft you can see a visible yellow line stretching out from it used to keep the raft in position so it does not drift away.
When the mama megalodon eats Esai and the whole boat; you can clearly see as the shark's mouth emerges from the water that its teeth goes through the boat's motor showing that the hole scene is computer animated. Besides the boat is destroyed inside the shark's mouth and the shark has not even closed its mouth; in fact it never closes its mouth.
When Ben and Cat are chasing the shark back to the resort beach at minute 38:00 through minute 41:00, only the boats port shaft throttle is moved forward, multiple times, rather than both throttles. No indication of throttling back is shown. That means the boat would only do circles instead of actually going anywhere.
At minute 1:04 while the helicopter is hovering with a deployed chain ladder picking up rescuees, no disturbance is shown on the water. The helicopter downdraft will always show when hovering at that level.
When the three main characters are sitting at the table, the cameraman is reflected in the picture at the back of the room.
During the scene in which a young couple make-out whilst on a water slide, it can be easily noticed that at numerous points the shadow of the cameraman following the amorous couple can be seen cast on the edges of the slide.